No, the Punisher didn't knock him out. It was the Russian. However, Spider-Man should have been able to take the Russian relatively easily. It was Ennis showing his complete and utter disdain for super heroes that stuck in my craw. Was it funny? Yes, but it would have been funny without the inclusion of any super beings.

I've enjoyed much of Ennis's work, including his Punisher work, but every time he brings super heroes into the stories, they don't work so well.